void sample()
{
::fivox::URI uri = getURI();
// for compatibility
if( _vm.count( "size" ))
uri.addQuery( "size", std::to_string( _vm["size"].as< size_t >( )));
const ::fivox::URIHandler params( uri );
auto source = params.newImageSource< fivox::FloatVolume >();
const fivox::Vector3f& extent( source->getSizeInMicrometer( ));
const size_t size( std::ceil( source->getSizeInVoxel().find_max( )));
const VolumeHandler volumeHandler( size, extent );
VolumePtr output = source->GetOutput();
output->SetRegions( volumeHandler.computeRegion( _decompose ));
output->SetSpacing( volumeHandler.computeSpacing( ));
const fivox::AABBf& bbox = source->getBoundingBox();
output->SetOrigin( volumeHandler.computeOrigin( bbox.getCenter( )));
::fivox::EventSourcePtr loader = source->getEventSource();
const fivox::Vector2ui frameRange( getFrameRange( loader->getDt( )));
const std::string& datatype( _vm["datatype"].as< std::string >( ));
if( datatype == "char" )
{
LBINFO << "Sampling volume as char (uint8_t) data" << std::endl;
_sample< uint8_t >( source, frameRange, params, _outputFile );
}
else if( datatype == "short" )
{
LBINFO << "Sampling volume as short (uint16_t) data" << std::endl;
_sample< uint16_t >( source, frameRange, params, _outputFile );
}
else if( datatype == "int" )
{
LBINFO << "Sampling volume as int (uint32_t) data" << std::endl;
_sample< uint32_t >( source, frameRange, params, _outputFile );
}
else
{
LBINFO << "Sampling volume as floating point data" << std::endl;
_sample< float >( source, frameRange, params, _outputFile );
}
}
std::string PointsFileSystem::getPointsFolder(int frame)
{
QModelIndex root_index = index(rootPath());
int start, end;
getFrameRange(start, end);
if (start < 0 || end < 0)
return std::string();
std::string folder;
QString root_path = rootPath();
if (root_path.contains("frame_"))
{
folder = root_path.toStdString();
}
else if (root_path.contains("points"))
{
// not work ??
/*std::cout << root_path.toStdString() << std::endl;
QModelIndex frame_index = index(frame-start, 0, root_index);
folder = filePath(frame_index).toStdString();*/
QString frame_name(QString("frame_%1").arg(frame, 5, 10, QChar('0')));
QStringList root_entries = QDir(root_path).entryList();
for (QStringList::const_iterator root_entries_it = root_entries.begin();
root_entries_it != root_entries.end(); ++ root_entries_it)
{
if (root_entries_it->compare(frame_name) == 0)
{
folder = (root_path + QString("/%1").arg(*root_entries_it)).toStdString();
break;
}
}
}
return folder;
}
void clip_t::getUnmappedFrameRange(double &unmappedStartFrame, double &unmappedEndFrame) const
{
getFrameRange( unmappedStartFrame, unmappedEndFrame);
}
// Parse parameter options from command line
bool setParams(int argc, char* argv[], LumaEncoderParams *params, IOData *io)
{
std::string frames;
std::string ptf, ptfValues[] = {"PSI", "PQ", "LOG", "HDRVDP", "LINEAR"}; // valid ptf input values
std::string cs, csValues[] = {"LUV", "RGB", "YCBCR", "XYZ"}; // valid color space input values
unsigned int bdValues[] = {8, 10, 12}; // valid bit depths
// Application usage info
std::string info = std::string("lumaenc -- Compress a sequence of high dyncamic range (HDR) frames in to a Matroska (.mkv) HDR video\n\n") +
std::string("Usage: lumaenc --input <hdr_frames> \\\n") +
std::string(" --frames <start_frame:step:end_frame> \\\n") +
std::string(" --output <output>\n");
std::string postInfo = std::string("\nExample: lumaenc -i hdr_frame_%05d.exr -f 1:100 -o hdr_video.mkv\n\n") +
std::string("See man page for more information.");
ArgParser argHolder(info, postInfo);
// Input arguments
argHolder.add(&io->hdrFrames, "--input", "-i", "Input HDR video sequence");
argHolder.add(&io->outputFile, "--output", "-o", "Output location of the compressed HDR video", 0);
argHolder.add(&frames, "--frames", "-f", "Input frames, formatted as startframe:step:endframe");
argHolder.add(¶ms->fps, "--framerate", "-fps", "Framerate of video stream, specified as frames/s");
argHolder.add(¶ms->profile, "--profile", "-p", "VP9 encoding profile", (unsigned int)(0), (unsigned int)(3));
argHolder.add(¶ms->quantizerScale, "--quantizer-scaling", "-q", "Scaling of the encoding quantization", (unsigned int)(0), (unsigned int)(63));
argHolder.add(¶ms->preScaling, "--pre-scaling", "-sc", "Scaling of pixels to apply before tranformation and encoding", 0.0f, 1e20f);
argHolder.add(¶ms->ptfBitDepth, "--ptf-bitdepth", "-pb", "Bit depth of the perceptual transfer function", (unsigned int)(0), (unsigned int)(16));
argHolder.add(¶ms->colorBitDepth, "--color-bitdepth", "-cb", "Bit depth of the color channels", (unsigned int)(0), (unsigned int)(16));
argHolder.add(&ptf, "--transfer-function", "-ptf", "The perceptual transfer function used for encoding", ptfValues, 5);
argHolder.add(&cs, "--color-space", "-cs", "Color space for encoding", csValues, 4);
argHolder.add(¶ms->bitrate, "--bitrate", "-b", "HDR video stream target bandwidth, in Kb/s", (unsigned int)(0), (unsigned int)(9999));
argHolder.add(¶ms->keyframeInterval, "--keyframe-interval", "-k", "Interval between keyframes. 0 for automatic keyframes", (unsigned int)(0), (unsigned int)(9999));
argHolder.add(¶ms->bitDepth, "--encoding-bitdepth", "-eb", "Encoding at 8, 10 or 12 bits", bdValues, 3);
argHolder.add(¶ms->lossLess, "--lossless", "-l", "Enable lossless encoding mode");
argHolder.add(&io->verbose, "--verbose", "-v", "Verbose mode");
// Parse arguments
if (!argHolder.read(argc, argv))
return 0;
// Check output format
if (!hasExtension(io->outputFile.c_str(), ".mkv"))
throw ParserException("Unsupported output format. HDR video should be stored as Matroska file (.mkv)");
// Parse frame range
if (frames.size() > 0 && !getFrameRange(frames, io->startFrame, io->stepFrame, io->endFrame))
throw ParserException(std::string("Unable to parse frame range from '" + frames + "'. Valid format is startframe:step:endframe").c_str());
// Valid frame range?
if (io->endFrame < io->startFrame)
throw ParserException(std::string("Invalid frame range '" + frames + "'. End frame should be >= start frame").c_str());
// Translate input strings to enums
if (!strcmp(ptf.c_str(), ptfValues[0].c_str()))
params->ptf = LumaQuantizer::PTF_PSI;
else if (!strcmp(ptf.c_str(), ptfValues[1].c_str()))
params->ptf = LumaQuantizer::PTF_PQ;
else if (!strcmp(ptf.c_str(), ptfValues[2].c_str()))
params->ptf = LumaQuantizer::PTF_LOG;
else if (!strcmp(ptf.c_str(), ptfValues[3].c_str()))
params->ptf = LumaQuantizer::PTF_JND_HDRVDP;
else if (!strcmp(ptf.c_str(), ptfValues[4].c_str()))
params->ptf = LumaQuantizer::PTF_LINEAR;
if (!strcmp(cs.c_str(), csValues[0].c_str()))
params->colorSpace = LumaQuantizer::CS_LUV;
else if (!strcmp(cs.c_str(), csValues[1].c_str()))
params->colorSpace = LumaQuantizer::CS_RGB;
else if (!strcmp(cs.c_str(), csValues[2].c_str()))
params->colorSpace = LumaQuantizer::CS_YCBCR;
else if (!strcmp(cs.c_str(), csValues[3].c_str()))
params->colorSpace = LumaQuantizer::CS_XYZ;
return 1;
}
void sample()
{
::fivox::URI uri = getURI();
const size_t sensorRes( _vm["sensor-res"].as< size_t >( ));
const size_t sensorDim( _vm["sensor-dim"].as< size_t >( ));
const float resolution = (float)sensorDim / sensorRes;
// the URI handler takes voxels/unit as resolution
uri.addQuery( "resolution", std::to_string( 1 / resolution ));
const ::fivox::URIHandler params( uri );
ImageSourcePtr source = params.newImageSource< fivox::FloatVolume >();
_eventSource = source->getEventSource();
std::shared_ptr< fivox::VSDLoader > vsdLoader =
std::static_pointer_cast< fivox::VSDLoader >( _eventSource );
const float v0 = _vm["v0"].as< float >();
const float g0 = _vm["g0"].as< float >();
LBINFO << "VSD info: V0 = " << v0 << " mV; G0 = " << g0 << std::endl;
vsdLoader->setRestingPotential( v0 );
vsdLoader->setAreaMultiplier( g0 );
if( _vm.count( "ap-threshold" ))
{
vsdLoader->setSpikeFilter( true );
const float apThreshold = _vm["ap-threshold"].as< float >();
LBINFO << "Action potential threshold set to " << apThreshold
<< " mV." << std::endl;
vsdLoader->setApThreshold( apThreshold );
}
if( _vm.count( "curve" ))
{
const std::string& curveFile = _vm["curve"].as< std::string >();
const float depth = _vm["depth"].as< float >();
const bool interpolate = _vm.count( "interpolate-attenuation" );
LBINFO << "Using '" << curveFile << "' as the dye curve file; "
<< "depth of " << depth << " micrometers. "
<< "Attenuation values will" << (!interpolate ? " not " :" ")
<< "be interpolated." << std::endl;
const fivox::AttenuationCurve dye( curveFile, depth );
vsdLoader->setCurve( dye );
vsdLoader->setInterpolation( interpolate );
}
const size_t size( std::ceil( source->getSizeInVoxel().find_max( )));
// crop the volume region to the specified sensor dimensions
fivox::Vector3f extent( source->getSizeInMicrometer( ));
extent[0] = sensorDim;
extent[2] = sensorDim;
const fivox::VolumeHandler volumeHandler( size, extent );
fivox::FloatVolume::IndexType vIndex;
vIndex.Fill(0);
fivox::FloatVolume::SizeType vSize;
vSize[0] = extent[0] / resolution;
vSize[1] = extent[1] / resolution;
vSize[2] = extent[2] / resolution;
VolumePtr output = source->GetOutput();
output->SetRegions( fivox::FloatVolume::RegionType( vIndex, vSize ));
fivox::AABBf bboxSomas;
const auto& somaPositions = vsdLoader->getSomaPositions();
for( const auto& position : somaPositions )
bboxSomas.merge( position );
// pixel/voxel size
const auto spacing = volumeHandler.computeSpacing();
// left bottom corner of the image/volume
const auto origin = volumeHandler.computeOrigin( bboxSomas.getCenter());
if( _vm.count( "soma-pixels" ))
{
const auto& fileName = _vm["soma-pixels"].as< std::string >();
std::ofstream file( fileName );
if( !file.is_open( ))
LBERROR << "File " << fileName << " could not be opened"
<< std::endl;
else
{
file << "# Soma position and corresponding pixel index for "
"each cell, in the following format:\n"
<< "# gid [ posX posY posZ ]: i j\n"
<< "# File version: 1\n"
<< "# Fivox version: " << fivox::Version::getString()
<< std::endl;
size_t i = 0;
const auto& gids = vsdLoader->getGIDs();
for( const auto& gid : gids )
{
if( file.bad( ))
break;
const auto& pos = somaPositions[i++];
file << gid << " " << pos << ": "
<< std::floor((pos[0] - origin[0]) / spacing[0]) << " "
<< std::floor((pos[2] - origin[2]) / spacing[1])
<< std::endl;
}
}
if( file.good( ))
LBINFO << "Soma positions written as " << fileName << std::endl;
else
LBERROR << "Error while writing to " << fileName << std::endl;
}
output->SetSpacing( spacing );
output->SetOrigin( origin );
VolumeWriter< float > writer( output, fivox::Vector2ui( ));
const fivox::Vector2ui frameRange( getFrameRange( _eventSource->getDt( )));
size_t numDigits = std::to_string( frameRange.y( )).length();
if( _vm.count( "times" ))
{
const float endTime = _vm["times"].as< fivox::Vector2f >()[1];
std::ostringstream s;
s << std::fixed << std::setprecision(1) << endTime;
numDigits = s.str().length();
}
if( _vm.count( "export-point-sprites" ))
{
_writePointSpriteHeader();
_writePointSpritePositions();
}
for( uint32_t i = frameRange.x(); i < frameRange.y(); ++i )
{
std::string filename = _outputFile;
if( frameRange.y() - frameRange.x() > 1 )
{
// append the frame number if --frames, timestamp otherwise
std::ostringstream os;
os << filename << std::setfill('0') << std::setw( numDigits );
if( _vm.count( "times" ))
os << std::fixed << std::setprecision(1)
<< i * vsdLoader->getDt();
else
os << i;
filename = os.str();
}
_eventSource->setFrame( i );
source->Modified();
if( _vm.count( "export-volume" ))
{
const std::string& volumeName = filename + ".mhd";
writer->SetFileName( volumeName );
source->Modified();
writer->Update(); // Run pipeline to write volume
LBINFO << "Volume written as " << volumeName << std::endl;
}
projectVSD( output, filename );
if( _vm.count( "export-point-sprites" ))
_writePointSpriteIntensities( filename );
}
}
OfxRangeD getFrameRange() const
{
OfxRangeD frameRange;
getFrameRange( frameRange.min, frameRange.max );
return frameRange;
}